A proprietary OmniPlex(tm) technology will be optimized to prepare amplified DNA and RNA samples from formalin-fixed, paraffin-embedded (FFPE) tissues. These OmniPlex products will have predictable performance in downstream applications and allow meaningful genome-wide genetic and gene expression analyses of formalin-fixed tumor specimens for cancer research and diagnostics. These analyses are currently challenging, because no technology can effectively amplify FFPE DNA and RNA samples of variable quality and produce amplified samples with predictable, standardized quality. In the basic OmniPlex process, high quality DNA and RNA samples from fresh tissues and cultured cells are amplified with robust and reproducible efficiencies, but FFPE samples are frequently damaged and/or degraded and amplify with unpredictable and highly variable efficiencies. In Phase I the basic OmniPlex process will be modified in order to produce more robust and reproducible FFPE sample amplification efficiencies, which are required for producing amplified products with predictable, standardized quality. Specific Aim 1 is to identify a real-time quantitative PCR assay that will normalize input FFPE DNA sample amounts better than mass measurements. Specific Aim 2 is to improve the conversion of FFPE samples to amplifiable OmniPlex libraries by modifying reagent and incubation conditions. Finally, Specific Aim 3 is to use in-house quantitative PCR assays to develop quality parameters that predict amplified FFPE sample performance in genetic and gene expression studies. Successful Phase I project results will lead to Phase II studies that test the robustness of the improved process on a large set of normal and tumor samples, uniquely allow DNA and RNA amplification from the same samples, and demonstrate the utility of amplified FFPE samples for cancer research on major commercial genetic and gene expression platforms. The potential commercial applications of this research will be OmniPlex FFPE amplification kits and amplification service projects.